School of Mathematics and Statistics - Research Publications

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    A model for analyzing clustered occurrence data
    Hwang, W-H ; Huggins, R ; Stoklosa, J (WILEY, 2021-02-15)
    Spatial or temporal clustering commonly arises in various biological and ecological applications, for example, species or communities may cluster in groups. In this paper, we develop a new clustered occurrence data model where presence-absence data are modeled under a multivariate negative binomial framework. We account for spatial or temporal clustering by introducing a community parameter in the model that controls the strength of dependence between observations thereby enhancing the estimation of the mean and dispersion parameters. We provide conditions to show the existence of maximum likelihood estimates when cluster sizes are homogeneous and equal to 2 or 3 and consider a composite likelihood approach that allows for additional robustness and flexibility in fitting for clustered occurrence data. The proposed method is evaluated in a simulation study and demonstrated using forest plot data from the Center for Tropical Forest Science. Finally, we present several examples using multiple visit occupancy data to illustrate the difference between the proposed model and those of N-mixture models.
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    Information content of stepped wedge designs with unequal cluster-period sizes in linear mixed models: Informing incomplete designs.
    Kasza, J ; Bowden, R ; Forbes, AB (Wiley, 2021-03-30)
    In practice, stepped wedge trials frequently include clusters of differing sizes. However, investigations into the theoretical aspects of stepped wedge designs have, until recently, typically assumed equal numbers of subjects in each cluster and in each period. The information content of the cluster-period cells, clusters, and periods of stepped wedge designs has previously been investigated assuming equal cluster-period sizes, and has shown that incomplete stepped wedge designs may be efficient alternatives to the full stepped wedge. How this changes when cluster-period sizes are not equal is unknown, and we investigate this here. Working within the linear mixed model framework, we show that the information contributed by design components (clusters, sequences, and periods) does depend on the sizes of each cluster-period. Using a particular trial that assessed the impact of an individual education intervention on log-length of stay in rehabilitation units, we demonstrate how strongly the efficiency of incomplete designs depends on which cells are excluded: smaller incomplete designs may be more powerful than alternative incomplete designs that include a greater total number of participants. This also serves to demonstrate how the pattern of information content can be used to inform a set of incomplete designs to be considered as alternatives to the complete stepped wedge design. Our theoretical results for the information content can be extended to a broad class of longitudinal (ie, multiple period) cluster randomized trial designs.
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    Sex-Dependent Shared and Nonshared Genetic Architecture Across Mood and Psychotic Disorders
    Blokland, GAM ; Grove, J ; Chen, C-Y ; Cotsapas, C ; Tobet, S ; Handa, R ; St Clair, D ; Lencz, T ; Mowry, BJ ; Periyasamy, S ; Cairns, MJ ; Tooney, PA ; Wu, JQ ; Kelly, B ; Kirov, G ; Sullivan, PF ; Corvin, A ; Riley, BP ; Esko, T ; Milani, L ; Jonsson, EG ; Palotie, A ; Ehrenreich, H ; Begemann, M ; Steixner-Kumar, A ; Sham, PC ; Iwata, N ; Weinberger, DR ; Gejman, P ; Sanders, AR ; Buxbaum, JD ; Rujescu, D ; Giegling, I ; Konte, B ; Hartmann, AM ; Bramon, E ; Murray, RM ; Pato, MT ; Lee, J ; Melle, I ; Molden, E ; Ophoff, RA ; McQuillin, A ; Bass, NJ ; Adolfsson, R ; Malhotra, AK ; Martin, NG ; Fullerton, JM ; Mitchell, PB ; Schofield, PR ; Forstner, AJ ; Degenhardt, F ; Schaupp, S ; Comes, AL ; Kogevinas, M ; Guzman-Parra, J ; Reif, A ; Streit, F ; Sirignano, L ; Cichon, S ; Grigoroiu-Serbanescu, M ; Hauser, J ; Lissowska, J ; Mayoral, F ; Muller-Myhsok, B ; Schulze, TG ; Nothen, MM ; Rietschel, M ; Kelsoe, J ; Leboyer, M ; Jamain, S ; Etain, B ; Bellivier, F ; Vincent, JB ; Alda, M ; O'Donovan, C ; Cervantes, P ; Biernacka, JM ; Frye, M ; McElroy, SL ; Scott, LJ ; Stahl, EA ; Landen, M ; Hamshere, ML ; Smeland, OB ; Djurovic, S ; Vaaler, AE ; Andreassen, OA ; Baune, BT ; Air, T ; Preisig, M ; Uher, R ; Levinson, DF ; Weissman, MM ; Potash, JB ; Shi, J ; Knowles, JA ; Perlis, RH ; Lucae, S ; Boomsma, D ; Penninx, BWJH ; Hottenga, J-J ; de Geus, EJC ; Willemsen, G ; Milaneschi, Y ; Tiemeier, H ; Grabe, HJ ; Teumer, A ; Van der Auwera, S ; Volker, U ; Hamilton, SP ; Magnusson, PKE ; Viktorin, A ; Mehta, D ; Mullins, N ; Adams, MJ ; Breen, G ; McIntosh, AM ; Lewis, CM ; Hougaard, DM ; Nordentoft, M ; Mors, O ; Mortensen, PB ; Werge, T ; Als, TD ; Borglum, AD ; Petryshen, TL ; Smoller, JW ; Goldstein, JM (ELSEVIER SCIENCE INC, 2021-11-29)
    BACKGROUND: Sex differences in incidence and/or presentation of schizophrenia (SCZ), major depressive disorder (MDD), and bipolar disorder (BIP) are pervasive. Previous evidence for shared genetic risk and sex differences in brain abnormalities across disorders suggest possible shared sex-dependent genetic risk. METHODS: We conducted the largest to date genome-wide genotype-by-sex (G×S) interaction of risk for these disorders using 85,735 cases (33,403 SCZ, 19,924 BIP, and 32,408 MDD) and 109,946 controls from the PGC (Psychiatric Genomics Consortium) and iPSYCH. RESULTS: Across disorders, genome-wide significant single nucleotide polymorphism-by-sex interaction was detected for a locus encompassing NKAIN2 (rs117780815, p = 3.2 × 10-8), which interacts with sodium/potassium-transporting ATPase (adenosine triphosphatase) enzymes, implicating neuronal excitability. Three additional loci showed evidence (p < 1 × 10-6) for cross-disorder G×S interaction (rs7302529, p = 1.6 × 10-7; rs73033497, p = 8.8 × 10-7; rs7914279, p = 6.4 × 10-7), implicating various functions. Gene-based analyses identified G×S interaction across disorders (p = 8.97 × 10-7) with transcriptional inhibitor SLTM. Most significant in SCZ was a MOCOS gene locus (rs11665282, p = 1.5 × 10-7), implicating vascular endothelial cells. Secondary analysis of the PGC-SCZ dataset detected an interaction (rs13265509, p = 1.1 × 10-7) in a locus containing IDO2, a kynurenine pathway enzyme with immunoregulatory functions implicated in SCZ, BIP, and MDD. Pathway enrichment analysis detected significant G×S interaction of genes regulating vascular endothelial growth factor receptor signaling in MDD (false discovery rate-corrected p < .05). CONCLUSIONS: In the largest genome-wide G×S analysis of mood and psychotic disorders to date, there was substantial genetic overlap between the sexes. However, significant sex-dependent effects were enriched for genes related to neuronal development and immune and vascular functions across and within SCZ, BIP, and MDD at the variant, gene, and pathway levels.
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    Fluctuations of the number of excursion sets of planar Gaussian fields
    Beliaev, D ; McAuley, M ; Muirhead, S (Mathematical Sciences Publishers, 2022-05-11)
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    Early life infection and proinflammatory, atherogenic metabolomic and lipidomic profiles in infancy: a population-based cohort study.
    Mansell, T ; Saffery, R ; Burugupalli, S ; Ponsonby, A-L ; Tang, MLK ; O'Hely, M ; Bekkering, S ; Smith, AAT ; Rowland, R ; Ranganathan, S ; Sly, PD ; Vuillermin, P ; Collier, F ; Meikle, P ; Burgner, D ; Barwon Infant Study Investigator Group, (eLife Sciences Publications, Ltd, 2022-05-10)
    Background: The risk of adult onset cardiovascular and metabolic (cardiometabolic) disease accrues from early life. Infection is ubiquitous in infancy and induces inflammation, a key cardiometabolic risk factor, but the relationship between infection, inflammation, and metabolic profiles in early childhood remains unexplored. We investigated relationships between infection and plasma metabolomic and lipidomic profiles at age 6 and 12 months, and mediation of these associations by inflammation. Methods: Matched infection, metabolomics, and lipidomics data were generated from 555 infants in a pre-birth longitudinal cohort. Infection data from birth to 12 months were parent-reported (total infections at age 1, 3, 6, 9, and 12 months), inflammation markers (high-sensitivity C-reactive protein [hsCRP]; glycoprotein acetyls [GlycA]) were quantified at 12 months. Metabolic profiles were 12-month plasma nuclear magnetic resonance metabolomics (228 metabolites) and liquid chromatography/mass spectrometry lipidomics (776 lipids). Associations were evaluated with multivariable linear regression models. In secondary analyses, corresponding inflammation and metabolic data from birth (serum) and 6-month (plasma) time points were used. Results: At 12 months, more frequent infant infections were associated with adverse metabolomic (elevated inflammation markers, triglycerides and phenylalanine, and lower high-density lipoprotein [HDL] cholesterol and apolipoprotein A1) and lipidomic profiles (elevated phosphatidylethanolamines and lower trihexosylceramides, dehydrocholesteryl esters, and plasmalogens). Similar, more marked, profiles were observed with higher GlycA, but not hsCRP. GlycA mediated a substantial proportion of the relationship between infection and metabolome/lipidome, with hsCRP generally mediating a lower proportion. Analogous relationships were observed between infection and 6-month inflammation, HDL cholesterol, and apolipoprotein A1. Conclusions: Infants with a greater infection burden in the first year of life had proinflammatory and proatherogenic plasma metabolomic/lipidomic profiles at 12 months of age that in adults are indicative of heightened risk of cardiovascular disease, obesity, and type 2 diabetes. These findings suggest potentially modifiable pathways linking early life infection and inflammation with subsequent cardiometabolic risk. Funding: The establishment work and infrastructure for the BIS was provided by the Murdoch Children's Research Institute (MCRI), Deakin University, and Barwon Health. Subsequent funding was secured from National Health and Medical Research Council of Australia (NHMRC), The Shepherd Foundation, The Jack Brockhoff Foundation, the Scobie & Claire McKinnon Trust, the Shane O'Brien Memorial Asthma Foundation, the Our Women's Our Children's Fund Raising Committee Barwon Health, the Rotary Club of Geelong, the Minderoo Foundation, the Ilhan Food Allergy Foundation, GMHBA, Vanguard Investments Australia Ltd, and the Percy Baxter Charitable Trust, Perpetual Trustees. In-kind support was provided by the Cotton On Foundation and CreativeForce. The study sponsors were not involved in the collection, analysis, and interpretation of data; writing of the report; or the decision to submit the report for publication. Research at MCRI is supported by the Victorian Government's Operational Infrastructure Support Program. This work was also supported by NHMRC Senior Research Fellowships to ALP (1008396); DB (1064629); and RS (1045161) , NHMRC Investigator Grants to ALP (1110200) and DB (1175744), NHMRC-A*STAR project grant (1149047). TM is supported by an MCRI ECR Fellowship. SB is supported by the Dutch Research Council (452173113).
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    Molecular profiling reveals features of clinical immunity and immunosuppression in asymptomatic P. falciparum malaria
    Studniberg, S ; Ioannidis, LJ ; Utami, RAS ; Trianty, L ; Liao, Y ; Abeysekera, W ; Li-Wai-Suen, CSN ; Pietrzak, HM ; Healer, J ; Puspitasari, AM ; Apriyanti, D ; Coutrier, F ; Poespoprodjo, JR ; Kenangalem, E ; Andries, B ; Prayoga, P ; Sariyanti, N ; Smyth, GK ; Cowman, AF ; Price, RN ; Noviyanti, R ; Shi, W ; Garnham, AL ; Hansen, DS (WILEY, 2022-04-01)
    Clinical immunity to P. falciparum malaria is non-sterilizing, with adults often experiencing asymptomatic infection. Historically, asymptomatic malaria has been viewed as beneficial and required to help maintain clinical immunity. Emerging views suggest that these infections are detrimental and constitute a parasite reservoir that perpetuates transmission. To define the impact of asymptomatic malaria, we pursued a systems approach integrating antibody responses, mass cytometry, and transcriptional profiling of individuals experiencing symptomatic and asymptomatic P. falciparum infection. Defined populations of classical and atypical memory B cells and a TH2 cell bias were associated with reduced risk of clinical malaria. Despite these protective responses, asymptomatic malaria featured an immunosuppressive transcriptional signature with upregulation of pathways involved in the inhibition of T-cell function, and CTLA-4 as a predicted regulator in these processes. As proof of concept, we demonstrated a role for CTLA-4 in the development of asymptomatic parasitemia in infection models. The results suggest that asymptomatic malaria is not innocuous and might not support the induction of immune processes to fully control parasitemia or efficiently respond to malaria vaccines.
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    Consecutive level spacings in the chiral Gaussian unitary ensemble: from the hard and soft edge to the bulk
    Akemann, G ; Gorski, V ; Kieburg, M (IOP Publishing Ltd, 2022-05-13)
    Abstract The local spectral statistics of random matrices forms distinct universality classes, strongly depending on the position in the spectrum. Surprisingly, the spacing between consecutive eigenvalues at the spectral edges has received little attention, where the density diverges or vanishes, respectively. This different behaviour is called hard or soft edge. We show that the spacings at the edges are almost indistinguishable from the spacing in the bulk of the spectrum. We present analytical results for consecutive spacings between the kth and (k + 1)st smallest eigenvalues in the chiral Gaussian unitary ensemble, both for finite- and large-n. The result depends on the number of the generic zero modes ν and the number of flavours N f, which are given in terms of characteristic polynomials, as motivated by quantum chromodynamics (QCD). We find that the convergence in n is very rapid. The same can be said separately about the limit k → ∞ (limit to the bulk) and ν → ∞ (limit to the soft edge). Interestingly, the Wigner surmise is a very good approximation for all these cases and, apart from k = 1, shows a deviation below one percent. These findings are corroborated with Monte-Carlo simulations. We finally compare for k = 1 with data from QCD on the lattice, being in this symmetry class.
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    Interdependence of Software and Progress of Mathematics in OR: Some Illustrative Cases and Challenges
    Kumar, S ; Munapo, E (Scientific Research Publishing, Inc., 2021)
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    Does the duration of repeated temporary separation affect welfare in dairy cow-calf contact systems?
    Roadknight, N ; Wales, W ; Jongman, E ; Mansell, P ; Hepworth, G ; Fisher, A (Elsevier BV, 2022-04-01)
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    Estimation of the probability of epidemic fade-out from multiple outbreak data
    Alahakoon, P ; McCaw, JM ; Taylor, PG (ELSEVIER, 2022-03-01)
    Deterministic epidemic models that allow for replenishment of susceptibles typically display damped oscillatory behaviour. If the population is initially fully susceptible, once an epidemic takes off a distinct trough will exist between the first and second waves of infection. Epidemic dynamics are, however, influenced by stochastic effects, particularly when the prevalence is low. At the beginning of an epidemic, stochastic die-out is possible and well characterised through use of a branching process approximation. Conditional on an epidemic taking off, stochastic extinction is highly unlikely during the first epidemic wave, but the probability of extinction increases again as the wave declines. Extinction during this period, prior to a potential second wave of infection, is defined as 'epidemic fade-out'. We consider a set of observed epidemics, each distinct and having evolved independently, in which some display fade-out and some do not. While fade-out is necessarily a stochastic phenomenon, the probability of fade-out will depend on the model parameters associated with each epidemic. Accordingly, we ask whether time-series data for the epidemics contain sufficient information to identify the key driver(s) of different outcomes-fade-out or otherwise-across the sub-populations supporting each epidemic. We apply a Bayesian hierarchical modelling framework to synthetic data from an SIRS model of epidemic dynamics and demonstrate that we can (1) identify when the sub-population specific model parameters supporting each epidemic have significant variability and (2) estimate the probability of epidemic fade-out for each sub-population. We demonstrate that a hierarchical analysis can provide precise estimates of the probability of fade-out than is possible if considering each epidemic in isolation. Our methods may be applied to both epidemiological and other biological data to identify where differences in outcome-fade-out or recurrent infection/waves are purely due to chance or driven by underlying changes in the parameters driving the dynamics.